Always check --skip_pseudo_alignment and --pseudo_aligner are set

Author: drpatelh

conf/modules.config

@@ -1087,7 +1087,6 @@ if (!params.skip_multiqc) {
 
 if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'salmon') {
     process {
-
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:SALMON_QUANT' {
             ext.args   = { params.extra_salmon_quant_args ?: '' }
             publishDir = [
@@ -1112,7 +1111,7 @@ if (!params.skip_pseudo_alignment && params.pseudo_aligner == 'kallisto') {
     }
 }
 
-if (!params.skip_pseudo_alignment) {
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
     process {
         withName: '.*:QUANTIFY_PSEUDO_ALIGNMENT:TX2GENE' {
             publishDir = [

nextflow.config

@@ -58,7 +58,7 @@ params {
 
     // Alignment
     aligner                    = 'star_salmon'
-    pseudo_aligner             = 'salmon'
+    pseudo_aligner             = null
     seq_center                 = null
     bam_csi_index              = false
     star_ignore_sjdbgtf        = false

workflows/rnaseq.nf

@@ -37,13 +37,7 @@ if (!params.skip_bbsplit && !params.bbsplit_index && params.bbsplit_fasta_list)
 def prepareToolIndices  = []
 if (!params.skip_bbsplit) { prepareToolIndices << 'bbsplit' }
 if (!params.skip_alignment) { prepareToolIndices << params.aligner }
-if (!params.skip_pseudo_alignment) {
-    if(params.pseudo_aligner) { 
-        prepareToolIndices << params.pseudo_aligner 
-    } else {
-        exit 1, "--skip_pseudo_alignment not set, but --pseudo_aligner not set"
-    }
-}
+if (!params.skip_pseudo_alignment && params.pseudo_aligner) { prepareToolIndices << params.pseudo_aligner }
 
 // Determine whether to filter the GTF or not
 def filterGtf = 
@@ -822,9 +816,8 @@ workflow RNASEQ {
     //
     ch_pseudo_multiqc                   = Channel.empty()
     ch_pseudoaligner_pca_multiqc        = Channel.empty()
-    ch_pseudoaligner_clustering_multiqc = Channel.empty()
-    
-    if (!params.skip_pseudo_alignment) {
+    ch_pseudoaligner_clustering_multiqc = Channel.empty()    
+    if (!params.skip_pseudo_alignment && params.pseudo_aligner) {
 
        if (params.pseudo_aligner == 'salmon') {
            ch_pseudo_index = PREPARE_GENOME.out.salmon_index